Biology subjects

Maher, J. J.

Publications and source records attributed to Maher, J. J..

6 recordsLinked to original sources

bioRxiv2026

Humoral Immune Dysregulation Defines High-Risk Cirrhotic Ascites

Fluid accumulates within serosal cavities in diverse disease states, where it creates biologically active and potentially pathologic niches. How these expanded microenvironments reflect and shape disease biology remains incompletely resolved. Here, we investigated human ascites fluid (n = 118), a hallmark of decompensated cirrhosis, to determine whether signatures of microbial exposure and local host response distinguish outcomes. Cirrhotic ascites was characterized by barrier remodeling, depletion of plasma cell-associated programs, and enrichment of oropharyngeal microbes. Surprisingly, detection of oropharyngeal microbes in ascites was not associated with adverse outcomes. Instead, the ascites of cirrhotic patients with poor outcomes was marked by profound plasma cell depletion and significantly reduced dimeric IgA, despite the presence of antigen-experienced B cells. Together, these findings identify local B cell dysregulation as a previously underappreciated component of cirrhosis-associated immune dysfunction. Impaired local humoral immunity, rather than microbial translocation alone, emerges as a feature of high-risk decompensated cirrhosis.

immunology↗

bioRxiv2025

iPSC-Derived Hepatocytes from Patients with MASLD Exhibit Early Mitochondrial Dysfunction

Background & AimsA hallmark of metabolic dysfunction-associated steatotic liver disease (MASLD) is a decline in the ability of hepatocyte mitochondria to adapt to excess lipid. This leads to the production of reactive oxygen species (ROS) and the instigation of a vicious cycle of further mitochondrial damage and cellular dysfunction that promotes disease progression. In this study, we investigated whether induced pluripotent stem cells (iPSCs) from MASLD patients exhibit features of mitochondrial dysfunction when differentiated to hepatocyte-like cells (iPSC-Heps). MethodsiPSCs from 10 MASLD patients and 10 healthy control subjects genotyped for the I148M variant of PNPLA3 were differentiated to iPSC-Heps. Mitochondrial mass and function were assessed under basal culture conditions and following short-term exposure to exogenous palmitate. Outcomes included gene expression, mitochondrial oxygen consumption, ROS production and cellular energy status. ResultsiPSC-Heps from MASLD patients spontaneously accrued more lipid than control iPSC-Heps. Mitochondrial content was similar in MASLD and control iPSC-Heps, but MASLD iPSC-Heps displayed significant differences in mitochondrial function including a decrease in oxygen consumption rate when challenged with palmitate. Antioxidant gene expression was increased at baseline in MASLD vs. control iPSC-Heps, and MASLD iPSC-Heps produced more ROS and less ATP than controls after palmitate treatment. Differences persisted even when controlling for PNPLA3 genotype. ConclusionsiPSC-Heps from MASLD patients exhibit mitochondrial alterations characteristic of their diseased origin. The degree of mitochondrial dysfunction seen in MASLD iPSC-Heps is reminiscent of that described clinically in early MASLD, prior to progression to steatohepatitis. Mitochondrial alterations in MASLD iPSC-Heps occur independently of PNPLA3 genotype.

cell biology↗

bioRxiv2025

Predicting Metabolic Dysfunction Associated Steatotic Liver Disease Risk Using Patient-Derived Induced Pluripotent Stem Cells

Background and AimsMetabolic Dysfunction Associated Steatotic Liver Disease (MASLD) is reversible at early stages, making early identification of high-risk individuals clinically valuable. Previously, we demonstrated that patient-derived induced pluripotent stem cells (iPSCs) harboring MASLD DNA risk variants exhibit greater oleate-induced intracellular lipid accumulation than those without these variants. This study aimed to develop an iPSC-based MASLD risk predictor using functional lipid accumulation assessments. MethodsWe quantified oleate-induced intracellular lipid accumulation in iPSCs derived from three cohorts of diverse ancestry: 1) CIRM cohort (20 biopsy-confirmed MASH cases, 2 biopsy-confirmed MASLD cases, 17 controls), 2) POST cohort (18 MASLD cases, 17 controls), and 3) UCSF cohort (4 biopsy-confirmed MASH cases, 8 controls). Lipid accumulation levels in the CIRM cohort were used to define an iPSC-based MASLD risk score, which was used to predict case/control status in the POST and UCSF cohorts. ResultsIn all three cohorts, lipid accumulation was higher in MASLD/MASH cases vs. controls (CIRM cases vs. controls 3.32 {+/-} 0.25 vs. 2.70 {+/-} 0.19 -fold change, p=0.06; POST cases vs. controls 3.63 {+/-} 0.33 vs. 2.70 {+/-} 0.31, p=0.05; and UCSF cases vs. controls 4.39{+/-}0.46 vs. 2.03{+/-}0.20, p=0.0002). The iPSC-based MASLD risk score achieved a sensitivity of 44% and specificity of 75% in the POST cohort and 75% and 100%, respectively, in the UCSF cohort. Differences in cohort disease severity and cardiometabolic profiles may explain performance variability. ConclusionWhile validation in larger cohorts is needed, these findings suggest that oleate-induced intracellular lipid accumulation in subject-derived iPSCs is predictive of MASH development. Additional cellular phenotypes and donor information should be explored to improve predictive accuracy to inform MASLD surveillance and prevention strategies.

cell biology↗

bioRxiv2020

Hepatocyte-specific deletion of XBP1 sensitizes mice to liver injury through hyperactivation of IRE1α

X-box binding protein-1 (XBP1) is a transcription factor that plays a central role in controlling cellular responses to endoplasmic reticulum (ER) stress. Under stress conditions, the transcriptionally active form of XBP1 is generated by unique splicing of Xbp1 mRNA by the ER-resident protein inositol-requiring enzyme-1 (IRE1). Genetic deletion of XBP1 has multiple consequences: some resulting from the loss of the transcription factor per se, and others related to compensatory upstream activation of IRE1. The objective of the current study was to investigate the effects of XBP1 deletion in adult mouse liver and determine to what extent they are direct or indirect. XBP1 was deleted specifically from hepatocytes in adult Xbp1fl/fl mice using AAV8-Transthyretin-Cre (Xbp1{Delta}hep). Xbp1{Delta}hep mice exhibited no liver disease at baseline, but developed acute biochemical and histologic liver injury in response to a dietary challenge with fructose for 4 wk. Fructose-mediated liver injury in Xbp1{Delta}hep mice coincided with heightened IRE1 activity, as demonstrated by cJun phosphorylation and regulated IRE1 -dependent RNA decay (RIDD). Activation of eIF2 was also evident, with associated up-regulation of the pro-apoptotic molecules CHOP, BIM and PUMA. To determine whether the adverse consequences of liver-specific XBP1 deletion were due to XBP1 loss or heightened IRE1 activity, we repeated a fructose challenge in mice with liver-specific deletion of both XBP1 and IRE1 (Xbp1{Delta}hep;IRE1{Delta}hep). Xbp1{Delta}hep;IRE1{Delta}hep mice were protected from fructose-mediated liver injury and failed to exhibit any of the signs of ER stress seen in mice lacking XBP1 alone. The protective effect of IRE1 deletion persisted even with long-term exposure to fructose. Xbp1{Delta}hep mice developed liver fibrosis at 16 wk, but Xbp1{Delta}hep;IRE1{Delta}hep mice did not. Overall, the results indicate that the deleterious effects of hepatocyte-specific XBP1 deletion are due primarily to hyperactivation of IRE1. They support further exploration of IRE1 as a contributor to acute and chronic liver diseases.

cell biology↗

bioRxiv2020

iPSC-derived hepatocytes from patients with nonalcoholic fatty liver disease display a disease-specific gene expression profile

Nonalcoholic fatty liver disease (NAFLD) is one of the leading causes of liver disease worldwide.1 Animal models are widely used to investigate the mechanisms of fatty liver disease, but they do not faithfully represent NAFLD in humans.2 Thus, there is strong interest in studying NAFLD pathogenesis directly in humans whenever possible. One strategy that is gaining momentum is to utilize iPSC-derived hepatocytes from individual human subjects in complex cell/organ platforms with the goal of reproducing a NAFLD-like state in vitro.3-6 Our group has taken a different approach, positing that iPSC-Heps from a population of NAFLD patients would provide independent insight into the human disease. In this study we generated iPSCs and iPSC-Heps from a well-defined cohort of NAFLD patients. Our objective was to determine whether as a group, in the absence of any metabolic challenge, they exhibit common disease-specific signatures that are distinct from healthy controls.Competing Interest StatementThis work was funded by research grants from the California Institute for Regenerative Medicine (IT1-06563), AbbVie, Inc. and NIH: R21 DK118380 (JJM), UG3 DK120004 (HW) and K08 DK098270 (ANM). Additional support was provided by core facilities within the UCSF Liver Center (P30 DK026743).View Full Text

pathology↗

bioRxiv2020

Doxycycline Significantly Enhances Induction of iPSCs to Endoderm by Enhancing survival via AKT Phosphorylation

Induced pluripotent stem cells (iPSCs) provide an important tool for the generation patient-derived cells including hepatocyte-like cells via developmental cues through an endoderm intermediate. However, most iPSCs fail to differentiate into endoderm, with induction resulting in apoptosis. To address this issue, we built upon published methods to develop an improved protocol with our discovery that doxycycline dramatically enhances the iPSC to endoderm differentiation efficiency by inhibiting apoptosis and promoting proliferation via the AKT pathway. We tested this new protocol in more than 70 iPSC lines with consistent formation of complete sheets of endoderm in 90%. Endoderm generated by our method achieves similar transcriptomic profiles, including FOXA2, HNF1{beta}, CXCR4, and SOX17 positive cells, and the ability to be further differentiated. Furthermore this method achieves a four-fold increase in endoderm cell number and will accelerate studies of human diseases in vitro and facilitate the expansion of iPSC-derived cells for transplantation studies.

developmental biology↗